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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAGAATTGCGGAAGTGGTTTCTCTCCATGGAGACTACACTTTTTCGGTATCGCTTTCGGCTTGAGAACCCTGAATCACAGgtgattttctataaatttatcatagaactgacaaaggaaaacaatttgtgtttatgctttaactgttgcttgttgcacaacatctgtttcag

Basic information

species Zea mays
transcript GRMZM2G130351_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G130351_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os07g22400.1 (Oryza sativa), 5'ss of exon 4
GGAAGAATTGCGGAAGTGGTTTCTCTCCATGGAGACTACACTTTTTCGGTATCGCTTTCGGCTTGAGAACCCTGAATCACAGgtgattttctataaatttatcatagaactgacaaaggaaaacaatttgtgtttatgctttaactgttgcttgttgcacaacatctgtttcag
||| ||  ||||||||||||||||||||||||||||||| |||||||| |||||||||||||| ||||  |||||||||||||||| ||||| |   ||| |   | |       ||||||| | ||        |||||||||| ||| ||||   |||   || |  |||||
GGAGGAGCTGCGGAAGTGGTTTCTCTCCATGGAGACTACGCTTTTTCGCTATCGCTTTCGGCTCGAGAGTCCTGAATCACAGgtgactttctgtccttttcttgcatac------aaggaaagctatc-------atgctttaaccgttccttgccacactgtattt--ttcag
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|78118655|gb|DV537039.1|DV537039
EST:     AGACTACACTTTTTCGGTATCGCTTTCGGCTTGAGAACCCTGAATCACAG                         AGGATGCTTATGACTGAGTTTCAACTGCCATACAAAGCATTGCCACACTCA
genomic: AGACTACACTTTTTCGGTATCGCTTTCGGCTTGAGAACCCTGAATCACAGgtgattttct ... tctgtttcagAGGATGCTTATGACTGAGTTTCAACTGCCATACAAAGCATTGCCACACTCA
EST: gi|149081470|gb|EE170604.2|EE170604
EST:     AGACTACACTTTTTCGGTATCGCTTTCGGCTTGAGAACCCTGAATCACAG                         AGGATGCTTATGACTGAGTTTCAACTGCCATACAAAGCATTGCCACACTCA
genomic: AGACTACACTTTTTCGGTATCGCTTTCGGCTTGAGAACCCTGAATCACAGgtgattttct ... tctgtttcagAGGATGCTTATGACTGAGTTTCAACTGCCATACAAAGCATTGCCACACTCA
EST: gi|91878919|gb|EB408876.1|EB408876
EST:     AGACTACACTTTTTCGGTATCGCTTTCGGCTTGAGAACCCTGAATCACAG                         AGGATGCTTATGACTG
genomic: AGACTACACTTTTTCGGTATCGCTTTCGGCTTGAGAACCCTGAATCACAGgtgattttct ... tctgtttcagAGGATGCTTATGACTG
EST: gi|89248072|gb|DY619858.1|DY619858
EST:     AGACTACACTTTTTCGGTATCGCTTTCGGCTTGAGAACCCTGAATCACAG                         AGGATGCTTATGACTG
genomic: AGACTACACTTTTTCGGTATCGCTTTCGGCTTGAGAACCCTGAATCACAGgtgattttct ... tctgtttcagAGGATGCTTATGACTG
EST: gi|110533099|gb|EE037279.1|EE037279
EST:     GACTACACTTTTTCGGTATCGCTTTCGGCTTGAGAACCCCTGAATCACAG                         AGGATGCTTATGACTGAGTTTCAACTGCCCTACCAAGCATTGCCCCACTCC
genomic: GACTACACTTTTTCGGTATCGCTTTCGGCTTGAGAACCC-TGAATCACAGgtgattttct ... tctgtttcagAGGATGCTTATGACTGAGTTTCAACTGCCATACAAAGCATTGCCACACTCA
EST: gi|148953215|gb|EE152697.2|EE152697
EST:     AGACTACACTTTTTCGGTATCGCTTTCGGCTTGAGAACCCTGAATCACAG                         AGGATGCTTATGACTGAGTTTCAACTGCCATACAAAGCATTGCCACACTCA
genomic: AGACTACACTTTTTCGGTATCGCTTTCGGCTTGAGAACCCTGAATCACAGgtgattttct ... tctgtttcagAGGATGCTTATGACTGAGTTTCAACTGCCATACAAAGCATTGCCACACTCA
EST: gi|76021633|gb|DT948803.1|DT948803
EST:     AGACTACACTTTTTCGGTATCGCTTTCGGCTTGAGAACCCTGAATCACAG                         AGGATGCTTATGACTGAGTTTCAACTGCCATACAAAGCATTGCCACACTCA
genomic: AGACTACACTTTTTCGGTATCGCTTTCGGCTTGAGAACCCTGAATCACAGgtgattttct ... tctgtttcagAGGATGCTTATGACTGAGTTTCAACTGCCATACAAAGCATTGCCACACTCA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 76

GGAAGAATTGCGGAAGTGGTTTCTCTCCATGGAGACTACACTTTTTCGGTATCGCTTTCGGCTTGAGAACCCTGAATCACAGgtgattttct ... tctgtttcagAGGATGCTTATGACTGAGTTTCAACTGCCATACAAAGCATTGCCACACTCAGAATTCGAG


Block sizes: 32 (upstream exon), 47 (downstream exon)
Score: 14

GGAAGAATTGCGGAAGTGGTTTCTCTCCATGGAGACTACACTTTTTCGGTATCGCTTTCGGCTTGAGAACCCTGAATCACAGgtgattttct ... tctgtttcagAGGATGCTTATGACTGAGTTTCAACTGCCATACAAAGCATTGCCACACTCAGAATTCGAG


Block sizes: 25 (upstream exon), 42 (downstream exon)
Score: 6

GGAAGAATTGCGGAAGTGGTTTCTCTCCATGGAGACTACACTTTTTCGGTATCGCTTTCGGCTTGAGAACCCTGAATCACAGgtgattttct ... tctgtttcagAGGATGCTTATGACTGAGTTTCAACTGCCATACAAAGCATTGCCACACTCAGAATTCGAG


Block sizes: 32 (upstream exon), 25 (downstream exon)
Score: 4

GGAAGAATTGCGGAAGTGGTTTCTCTCCATGGAGACTACACTTTTTCGGTATCGCTTTCGGCTTGAGAACCCTGAATCACAGgtgattttct ... tctgtttcagAGGATGCTTATGACTGAGTTTCAACTGCCATACAAAGCATTGCCACACTCAGAATTCGAG